synapsis
An R package to automate the analysis of double-strand break repair during meiosis
Bioconductor version: Release (3.17)
Synapsis is a Bioconductor software package for automated (unbiased and reproducible) analysis of meiotic immunofluorescence datasets. The primary functions of the software can i) identify cells in meiotic prophase that are labelled by a synaptonemal complex axis or central element protein, ii) isolate individual synaptonemal complexes and measure their physical length, iii) quantify foci and co-localise them with synaptonemal complexes, iv) measure interference between synaptonemal complex-associated foci. The software has applications that extend to multiple species and to the analysis of other proteins that label meiotic prophase chromosomes. The software converts meiotic immunofluorescence images into R data frames that are compatible with machine learning methods. Given a set of microscopy images of meiotic spread slides, synapsis crops images around individual single cells, counts colocalising foci on strands on a per cell basis, and measures the distance between foci on any given strand.
Author: Lucy McNeill [aut, cre, cph] 
, Wayne Crismani [rev, ctb]
Maintainer: Lucy McNeill <luc.mcneill at gmail.com>
citation("synapsis")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("synapsis")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("synapsis")| Using-synapsis | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | SingleCell, Software |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (2 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1) |
| Imports | EBImage, stats, utils, graphics |
| Linking To | |
| Suggests | knitr, rmarkdown, testthat (>= 3.0.0), ggplot2, tidyverse, BiocStyle |
| System Requirements | |
| Enhances | |
| URL |
See More
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | synapsis_1.6.0.tar.gz |
| Windows Binary | synapsis_1.6.0.zip |
| macOS Binary (x86_64) | synapsis_1.6.0.tgz |
| macOS Binary (arm64) | synapsis_1.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/synapsis |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/synapsis |
| Bioc Package Browser | https://code.bioconductor.org/browse/synapsis/ |
| Package Short Url | https://bioconductor.org/packages/synapsis/ |
| Package Downloads Report | Download Stats |